Conversion of fine organic surface mesh to a few patches of NURBS
You could write a python script in blender to import each stl in a folder, generate a cylindrical nurb surface around it (I am imagining long bone models like tibia and femur) and use the shrinkwrap modifier to approximate the tesselated surface of your STL model. Iges export would in theory keep the native surface nurb description intact for further cleanup in a solid modeling software, but in the past implementation in blender, it would chop the smooth surface up into polygons during export.

There is a lovely pure python nurb curve and surface library outside of Blender
https://nurbs-python.readthedocs.io/en/latest/index.html that might be helpful.